Last updated on 2025-12-21 11:50:45 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| BootstrapQTL | 4 | 1 | 8 |
| NetRep | 2 | 11 | |
| ukbnmr | 4 | 9 |
Current CRAN status: ERROR: 4, NOTE: 1, OK: 8
Version: 1.0.5
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Scott Ritchie <sritchie73@gmail.com>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = c("Qin", "Qin"),
family = "Huang",
role = "aut"),
person(given = "Scott",
family = "Ritchie",
role = c("aut", "cre"),
email = "sritchie73@gmail.com"))
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.0.5
Check: examples
Result: ERROR
Running examples in ‘BootstrapQTL-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BootstrapQTL
> ### Title: Bootstrap QTL analysis for accurate effect size estimation
> ### Aliases: BootstrapQTL
>
> ### ** Examples
>
> # Locations for example data from the MatrixEQTL package
> base.dir = find.package('MatrixEQTL');
> SNP_file_name = paste(base.dir, "/data/SNP.txt", sep="");
> snps_location_file_name = paste(base.dir, "/data/snpsloc.txt", sep="");
> expression_file_name = paste(base.dir, "/data/GE.txt", sep="");
> gene_location_file_name = paste(base.dir, "/data/geneloc.txt", sep="");
> covariates_file_name = paste(base.dir, "/data/Covariates.txt", sep="");
>
> # Load the SNP data
> snps = SlicedData$new();
> snps$fileDelimiter = "\t"; # the TAB character
> snps$fileOmitCharacters = "NA"; # denote missing values;
> snps$fileSkipRows = 1; # one row of column labels
> snps$fileSkipColumns = 1; # one column of row labels
> snps$fileSliceSize = 2000; # read file in slices of 2,000 rows
> snps$LoadFile(SNP_file_name);
Rows read: 15 done.
>
> # Load the data detailing the position of each SNP
> snpspos = read.table(snps_location_file_name, header = TRUE, stringsAsFactors = FALSE);
>
> # Load the gene expression data
> gene = SlicedData$new();
> gene$fileDelimiter = "\t"; # the TAB character
> gene$fileOmitCharacters = "NA"; # denote missing values;
> gene$fileSkipRows = 1; # one row of column labels
> gene$fileSkipColumns = 1; # one column of row labels
> gene$fileSliceSize = 2000; # read file in slices of 2,000 rows
> gene$LoadFile(expression_file_name);
Rows read: 10 done.
>
> # Load the data detailing the position of each gene
> genepos = read.table(gene_location_file_name, header = TRUE, stringsAsFactors = FALSE);
>
> # Load the covariates data
> cvrt = SlicedData$new();
> cvrt$fileDelimiter = "\t"; # the TAB character
> cvrt$fileOmitCharacters = "NA"; # denote missing values;
> cvrt$fileSkipRows = 1; # one row of column labels
> cvrt$fileSkipColumns = 1; # one column of row labels
> if(length(covariates_file_name)>0) {
+ cvrt$LoadFile(covariates_file_name);
+ }
Rows read: 2 done.
>
> # Run the BootstrapQTL analysis
> eQTLs <- BootstrapQTL(snps, gene, snpspos, genepos, cvrt, n_bootstraps=10, n_cores=2)
Registering 2 cores for bootstrap procedure.
Mapping QTLs and obtaining nominal effect size estimates...
10 of 10 genes matched
15 of 15 SNPs matched
100.00% done, 100 cis-eQTLs
Error in `[.data.table`(cis_assocs, , `:=`(local_pval, adjust_p(pvalue, :
attempt access index 6/6 in VECTOR_ELT
Calls: BootstrapQTL -> hierarchical_correction -> [ -> [.data.table
Restoring global environment...
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.0.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(BootstrapQTL)
Loading required package: MatrixEQTL
>
> test_check("BootstrapQTL")
Mapping QTLs and obtaining nominal effect size estimates...
Saving _problems/test-50.R
Restoring global environment...
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test.R:48:5'): Run BootstrapQTL ─────────────────────────────────────
Error in ``[.data.table`(cis_assocs, , `:=`(local_pval, adjust_p(pvalue, method = local)), by = gene)`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─base::tryCatch(...) at test.R:47:3
2. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
3. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
4. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
5. └─BootstrapQTL::BootstrapQTL(...) at test.R:48:5
6. └─BootstrapQTL:::hierarchical_correction(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [1s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(BootstrapQTL)
Loading required package: MatrixEQTL
>
> test_check("BootstrapQTL")
Mapping QTLs and obtaining nominal effect size estimates...
Saving _problems/test-50.R
Restoring global environment...
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test.R:48:5'): Run BootstrapQTL ─────────────────────────────────────
Error in ``[.data.table`(cis_assocs, , `:=`(local_pval, adjust_p(pvalue, method = local)), by = gene)`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─base::tryCatch(...) at test.R:47:3
2. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
3. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
4. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
5. └─BootstrapQTL::BootstrapQTL(...) at test.R:48:5
6. └─BootstrapQTL:::hierarchical_correction(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.5
Check: examples
Result: ERROR
Running examples in ‘BootstrapQTL-Ex.R’ failed
The error most likely occurred in:
> ### Name: BootstrapQTL
> ### Title: Bootstrap QTL analysis for accurate effect size estimation
> ### Aliases: BootstrapQTL
>
> ### ** Examples
>
> # Locations for example data from the MatrixEQTL package
> base.dir = find.package('MatrixEQTL');
> SNP_file_name = paste(base.dir, "/data/SNP.txt", sep="");
> snps_location_file_name = paste(base.dir, "/data/snpsloc.txt", sep="");
> expression_file_name = paste(base.dir, "/data/GE.txt", sep="");
> gene_location_file_name = paste(base.dir, "/data/geneloc.txt", sep="");
> covariates_file_name = paste(base.dir, "/data/Covariates.txt", sep="");
>
> # Load the SNP data
> snps = SlicedData$new();
> snps$fileDelimiter = "\t"; # the TAB character
> snps$fileOmitCharacters = "NA"; # denote missing values;
> snps$fileSkipRows = 1; # one row of column labels
> snps$fileSkipColumns = 1; # one column of row labels
> snps$fileSliceSize = 2000; # read file in slices of 2,000 rows
> snps$LoadFile(SNP_file_name);
Rows read: 15 done.
>
> # Load the data detailing the position of each SNP
> snpspos = read.table(snps_location_file_name, header = TRUE, stringsAsFactors = FALSE);
>
> # Load the gene expression data
> gene = SlicedData$new();
> gene$fileDelimiter = "\t"; # the TAB character
> gene$fileOmitCharacters = "NA"; # denote missing values;
> gene$fileSkipRows = 1; # one row of column labels
> gene$fileSkipColumns = 1; # one column of row labels
> gene$fileSliceSize = 2000; # read file in slices of 2,000 rows
> gene$LoadFile(expression_file_name);
Rows read: 10 done.
>
> # Load the data detailing the position of each gene
> genepos = read.table(gene_location_file_name, header = TRUE, stringsAsFactors = FALSE);
>
> # Load the covariates data
> cvrt = SlicedData$new();
> cvrt$fileDelimiter = "\t"; # the TAB character
> cvrt$fileOmitCharacters = "NA"; # denote missing values;
> cvrt$fileSkipRows = 1; # one row of column labels
> cvrt$fileSkipColumns = 1; # one column of row labels
> if(length(covariates_file_name)>0) {
+ cvrt$LoadFile(covariates_file_name);
+ }
Rows read: 2 done.
>
> # Run the BootstrapQTL analysis
> eQTLs <- BootstrapQTL(snps, gene, snpspos, genepos, cvrt, n_bootstraps=10, n_cores=2)
Registering 2 cores for bootstrap procedure.
Mapping QTLs and obtaining nominal effect size estimates...
10 of 10 genes matched
15 of 15 SNPs matched
100.00% done, 100 cis-eQTLs
Error in `[.data.table`(cis_assocs, , `:=`(local_pval, adjust_p(pvalue, :
attempt access index 6/6 in VECTOR_ELT
Calls: BootstrapQTL -> hierarchical_correction -> [ -> [.data.table
Restoring global environment...
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.5
Check: tests
Result: ERROR
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(BootstrapQTL)
Loading required package: MatrixEQTL
>
> test_check("BootstrapQTL")
Mapping QTLs and obtaining nominal effect size estimates...
Saving _problems/test-50.R
Restoring global environment...
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test.R:48:5'): Run BootstrapQTL ─────────────────────────────────────
Error in ``[.data.table`(cis_assocs, , `:=`(local_pval, adjust_p(pvalue, method = local)), by = gene)`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─base::tryCatch(...) at test.R:47:3
2. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
3. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
4. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
5. └─BootstrapQTL::BootstrapQTL(...) at test.R:48:5
6. └─BootstrapQTL:::hierarchical_correction(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
Error:
! Test failures.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.5
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: 'doMC'
Flavor: r-oldrel-windows-x86_64
Current CRAN status: NOTE: 2, OK: 11
Version: 1.2.9
Check: installed package size
Result: NOTE
installed size is 8.7Mb
sub-directories of 1Mb or more:
doc 1.7Mb
libs 5.9Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: ERROR: 4, OK: 9
Version: 3.3.1
Check: examples
Result: ERROR
Running examples in ‘ukbnmr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: remove_technical_variation
> ### Title: Remove technical variation from NMR biomarker data in UK
> ### Biobank.
> ### Aliases: remove_technical_variation
>
> ### ** Examples
>
> ukb_data <- ukbnmr::test_data # Toy example dataset for testing package
> processed <- remove_technical_variation(ukb_data)
Checking for revelant UKB fields...
Extracting and pre-processing data...
Checking for required sample processing fields needed for QC procedure...
Processing sample processing fields for QC procedure...
Error in `[.data.table`(sinfo, , `:=`(Spectrometer.Date.Bin, bin_dates(Plate.Measured.Date, :
attempt access index 17/17 in VECTOR_ELT
Calls: remove_technical_variation -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 3.3.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘ukbnmr.Rmd’ using rmarkdown
Quitting from ukbnmr.Rmd:115-121 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 17/17 in VECTOR_ELT
---
Backtrace:
▆
1. └─ukbnmr::remove_technical_variation(exported)
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'ukbnmr.Rmd' failed with diagnostics:
attempt access index 17/17 in VECTOR_ELT
--- failed re-building ‘ukbnmr.Rmd’
SUMMARY: processing the following file failed:
‘ukbnmr.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 3.3.1
Check: examples
Result: ERROR
Running examples in ‘ukbnmr-Ex.R’ failed
The error most likely occurred in:
> ### Name: remove_technical_variation
> ### Title: Remove technical variation from NMR biomarker data in UK
> ### Biobank.
> ### Aliases: remove_technical_variation
>
> ### ** Examples
>
> ukb_data <- ukbnmr::test_data # Toy example dataset for testing package
> processed <- remove_technical_variation(ukb_data)
Checking for revelant UKB fields...
Extracting and pre-processing data...
Checking for required sample processing fields needed for QC procedure...
Processing sample processing fields for QC procedure...
Error in `[.data.table`(sinfo, , `:=`(Spectrometer.Date.Bin, bin_dates(Plate.Measured.Date, :
attempt access index 17/17 in VECTOR_ELT
Calls: remove_technical_variation -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 3.3.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘ukbnmr.Rmd’ using rmarkdown
Quitting from ukbnmr.Rmd:115-121 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 17/17 in VECTOR_ELT
---
Backtrace:
▆
1. └─ukbnmr::remove_technical_variation(exported)
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'ukbnmr.Rmd' failed with diagnostics:
attempt access index 17/17 in VECTOR_ELT
--- failed re-building ‘ukbnmr.Rmd’
SUMMARY: processing the following file failed:
‘ukbnmr.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc